Variant report

Variant	rs12054398
Chromosome Location	chr3:85636185-85636186
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1025531	0.82[CHB][hapmap]
rs1030721	0.82[CHB][hapmap]
rs10511075	0.82[CHB][hapmap]
rs10511076	0.82[CHB][hapmap]
rs10511081	0.82[CHB][hapmap]
rs10511083	0.82[CHB][hapmap]
rs10865610	0.82[CHB][hapmap]
rs11127890	0.82[CHB][hapmap]
rs11127892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11127896	0.82[CHB][hapmap]
rs11919099	0.82[CHB][hapmap]
rs12485813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12486203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12486274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs12487886	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12488009	0.91[ASN][1000 genomes]
rs12488750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12491967	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs12492670	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12493440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12493445	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12493645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12495242	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12629291	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12631454	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12633762	0.82[CHB][hapmap]
rs12634226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12637214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12637236	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12638040	0.82[CHB][hapmap]
rs12638154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12638296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12639409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1368740	0.82[CHB][hapmap]
rs1375545	0.82[CHB][hapmap]
rs1375551	0.82[CHB][hapmap]
rs1375554	0.82[CHB][hapmap]
rs1375555	0.82[CHB][hapmap]
rs1375557	0.82[CHB][hapmap]
rs1449372	0.82[CHB][hapmap]
rs1449373	0.82[CHB][hapmap]
rs1449377	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1449380	0.82[CHB][hapmap]
rs1449382	0.82[CHB][hapmap]
rs1449387	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1449390	0.82[CHB][hapmap]
rs1449391	0.82[CHB][hapmap]
rs1449395	0.82[JPT][hapmap]
rs1449396	0.82[JPT][hapmap]
rs1449405	0.82[CHB][hapmap]
rs1449409	0.82[CHB][hapmap]
rs1463205	0.82[CHB][hapmap]
rs1463206	0.82[CHB][hapmap]
rs1463208	0.82[CHB][hapmap]
rs1470635	0.82[CHB][hapmap]
rs1530738	0.82[CHB][hapmap]
rs1530739	0.82[CHB][hapmap]
rs1530740	0.82[CHB][hapmap]
rs1597315	0.82[CHB][hapmap]
rs17022915	0.82[CHB][hapmap]
rs17023022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17456763	0.82[CHB][hapmap]
rs17459563	0.82[CHB][hapmap]
rs17460701	0.82[CHB][hapmap]
rs17516284	0.82[CHB][hapmap]
rs17516346	0.82[CHB][hapmap]
rs17517121	0.82[CHB][hapmap]
rs17518584	0.82[CHB][hapmap]
rs17519241	0.82[CHB][hapmap]
rs1868532	0.82[CHB][hapmap]
rs1900914	0.82[CHB][hapmap]
rs1900918	0.82[CHB][hapmap]
rs2029130	1.00[CHB][hapmap]
rs2029133	0.82[CHB][hapmap]
rs2122233	0.82[CHB][hapmap]
rs2326320	0.82[CHB][hapmap]
rs28626345	0.81[EUR][1000 genomes]
rs28673454	0.81[EUR][1000 genomes]
rs34193631	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441668	0.82[CHB][hapmap]
rs4502590	0.82[CHB][hapmap]
rs4856271	0.82[CHB][hapmap]
rs4856596	0.82[CHB][hapmap]
rs6549024	0.82[CHB][hapmap]
rs6549036	0.82[CHB][hapmap]
rs6549039	0.82[CHB][hapmap]
rs6549040	0.82[CHB][hapmap]
rs6549041	0.82[CHB][hapmap]
rs6549043	0.82[CHB][hapmap]
rs6762535	0.82[CHB][hapmap]
rs6762733	0.82[CHB][hapmap]
rs6766690	0.82[CHB][hapmap]
rs6767245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6767256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6767921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6788098	0.82[CHB][hapmap]
rs6790699	0.82[CHB][hapmap]
rs6791938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6794866	0.82[CHB][hapmap]
rs6801823	0.82[CHB][hapmap]
rs6804845	0.82[CHB][hapmap]
rs724304	0.82[CHB][hapmap]
rs7616458	0.82[CHB][hapmap]
rs7617356	0.82[CHB][hapmap]
rs7618429	0.82[CHB][hapmap]
rs7620313	0.82[CHB][hapmap]
rs7621463	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7634761	0.82[CHB][hapmap]
rs7643091	0.82[JPT][hapmap]
rs7653790	0.82[CHB][hapmap]
rs919874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs9309981	0.82[CHB][hapmap]
rs9309982	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs9309985	0.82[JPT][hapmap]
rs956281	0.82[CHB][hapmap]
rs9812845	0.82[JPT][hapmap]
rs9833314	0.82[CHB][hapmap]
rs9838811	0.82[CHB][hapmap];0.86[YRI][hapmap]
rs9864170	0.82[CHB][hapmap]
rs9880919	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1002238	chr3:85357855-85719373	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536619	chr3:85357855-85719373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590905	chr3:85438564-85797093	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv998829	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv536622	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv526621	chr3:85470642-85667683	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1009927	chr3:85497666-85669155	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1006360	chr3:85597755-85683081	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv536629	chr3:85597755-85683081	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1011376	chr3:85599411-85657771	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv590907	chr3:85619451-85694987	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv877101	chr3:85619451-85710336	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85634200-85636200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:85634400-85640800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:85634600-85636200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:85635600-85637800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:85636000-85637000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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